The obligations of the EU Biodiversity Strategy 2020 create a need for mapping and assessment of the state of biodiversity, ecosystems, and their services in all European member states. Europe’s nine outermost Regions (ORs) and 25 Overseas Countries and Territories (OCTs) are mainly islands, scattered around the globe. These territories contain unique flora and fauna and encompass diverse ecosystems, from coral reefs to rainforests. These highly diverse ecosystems provide multiple relevant ecosystem services from local to global scale. To date, the ecosystem services concept has so far received little attention in European ORs and OCTs. Therefore, our aims were (1) to analyze the current state of ecosystem services mapping and assessment in Europe’s overseas territories, (2) to identify knowledge gaps in the context of ecosystem service research and application, and (3) to provide recommendations for future research and policy directions to fill these gaps. We conducted a systematic review of scientific literature for each of the ORs and OCTs, screening 1030 publications. The analysis resulted in 161 publications referring to ES mapping and assessment, of which most were conducted in the European Caribbean (31%) and Pacific (21%) territories. Results show that many ORs and OCTs are still blank spots in terms of ecosystem service mapping and assessment and that, despite many biodiversity studies referring to species’ abundance, little has been published on ecosystem services. Our systematic review highlights the knowledge lacking in dealing with invasive species, which pose major threats to native island biodiversity, ecosystem functions, and ecosystem services. Further, it discusses knowledge gaps in (1) translation of the information on island biodiversity and ecosystem functions into ES; (2) geographical coverage of mapping studies in most ORs and OCTs; (3) the lack of standardized approaches and integrated assessments to map, assess and value ecosystem services. Based on these results, future research and policy priorities could be adapted in order to focus on filling these gaps. To overcome current environmental policy challenges, it is crucial to address the ongoing decline in biodiversity, rising climatic and anthropogenic pressures on ecosystems, and to maintain a sustainable ES flow to safeguard human well-being. Ultimately, ES mapping and assessment efforts will form the knowledge base for well-informed decision-making to protect Europe’s vulnerable overseas areas.